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The goal of tidysdm is to implement Species Distribution
Models using the tidymodels framework. The advantage of
tidymodels is that the model syntax and the results
returned to the user are standardised, thus providing a coherent
interface to modelling. Given the variety of models required for SDM,
tidymodels is an ideal framework. tidysdm
provides a number of wrappers and specialised functions to facilitate
the fitting of SDM with tidymodels.
Besides modelling contemporary species, tidysdm has a
number of functions specifically designed to work with palaeontological
data.
Whilst users are free to use their own environmental data, the
articles showcase the potential integration with pastclim,
which helps downloading and manipulating present day data, future
predictions, and palaeoclimate reconstructions.
An overview of the capabilities of tidysdm is given in
Leonardi et al.
(2023).
tidysdm is on CRAN, and the easiest way to install it is
with:
install.packages("tidysdm")The version on CRAN is recommended for every day use. New features
and bug fixes appear first on the dev branch on GitHub,
before they make their way to CRAN. If you need to have early access to
these new features, you can install tidysdm directly from
GitHub. To install from GitHub, you will need to use
devtools; if you haven’t done so already, get it from CRAN
with install.packages("devtools").
You can install the latest dev version of tidysdm from
GitHub with:
# install.packages("devtools")
devtools::install_github("EvolEcolGroup/tidysdm", ref = "dev")On its dedicated website, you can find Articles giving you a step-by-step overview of the fitting SDMs to contemporary species, as well as an equivalent tutorial for using palaeontological data. Furthermore, there is an Article with examples of how to leverage various features of tidymodels that are not commonly adopted in SDM pipelines
There is also a dev version of
the site updated for the dev branch of tidysdm
(on the top left of the dev website, the version number is in red and in
the format x.x.x.9xxx, indicating it is a development version). If you
want to contribute, make sure to read our contributing
guide.
What should you do if you get an error when trying to fit a model?
tidysdm is a relatively new package, so it might well be
that, when you get an error, you might have encountered a bug. However,
it is also possible that you have misspecified your model (and so the
error comes from tidymodels, because your model is not
valid). We have prepared an Article
on how to diagnose failing models. It is not a fully comprehensive
list of everything that could go wrong, but it will hopefully give you
ideas on how to dig deeper in what is wrong. You should also check the
issues on
GitHub to see whether the problem has already been reported.
If you are convinced that the problem is a bug in
tidysdm, feel free to create an new issue. Please make sure
you have updated to the latest version of tidysdm, as well
as updating all other packages on your system, and provide a
reproducible example for the developers to investigate the problem.
If you think you can help with fixing that bug, read our contributing
guide.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.